Contacts of the strand formed by residues 358 - 364 (chain I) in PDB entry 5BRR


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with PHE 358 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189I  PHE*     4.8     2.5    -      +       -      -
    237I  ILE*     3.9    24.7    -      -       +      -
    238I  ALA      3.5    15.7    -      -       -      +
    239I  ALA*     3.6    16.2    -      -       +      -
    247I  LEU*     3.4    15.5    -      -       -      +
    275I  LEU*     4.7     3.8    -      -       +      -
    276I  PRO*     4.2    13.7    -      -       +      -
    278I  PHE*     3.9    19.3    -      +       -      -
    354I  ILE*     3.5    23.3    -      -       +      -
    356I  ARG      3.4    15.3    -      -       -      -
    357I  PRO*     1.3    75.6    -      -       -      +
    359I  LEU*     1.3    71.8    +      -       -      +
    360I  PHE*     4.8     3.6    -      -       +      -
    376I  VAL*     2.6    72.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 359 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20I  PHE*     5.7     2.0    -      -       +      -
    221I  TYR*     5.1     1.6    -      -       +      -
    238I  ALA*     2.9    41.4    +      -       +      +
    247I  LEU*     3.5    39.3    -      -       +      +
    250I  LEU*     4.6    11.2    -      -       +      -
    251I  THR*     3.8    18.2    -      -       +      -
    254I  LEU*     3.6    36.3    -      -       +      -
    262I  TRP*     6.1     0.4    -      -       +      -
    358I  PHE*     1.3    83.1    -      -       -      +
    360I  PHE*     1.3    66.0    +      -       -      +
    361I  VAL*     5.6     0.2    -      -       +      -
    373I  MET*     5.7     0.2    -      -       +      -
    374I  GLY      2.8    22.4    -      -       -      +
    375I  GLN*     4.1     2.7    -      -       -      -
    376I  VAL      4.4     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 360 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33I  VAL*     4.0    19.1    -      -       +      -
    235I  MET*     3.9    34.5    -      -       +      -
    236I  PHE      3.1    13.2    -      -       -      +
    237I  ILE*     4.4     6.5    -      -       +      -
    238I  ALA*     5.8     0.2    -      -       -      -
    278I  PHE*     4.6    10.8    -      +       -      -
    326I  ILE*     4.1    15.0    -      -       +      -
    358I  PHE*     4.8     3.1    -      +       +      -
    359I  LEU*     1.3    82.3    -      -       -      +
    361I  VAL*     1.3    75.3    +      -       -      +
    362I  VAL*     4.0    17.0    -      -       +      -
    372I  PHE*     4.4     3.8    -      -       +      -
    373I  MET*     3.3    25.0    -      -       -      +
    374I  GLY*     3.1    45.7    +      -       -      -
    376I  VAL*     4.2    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 361 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234I  SER      3.8     0.3    -      -       -      +
    235I  MET*     3.3     3.1    -      -       -      +
    236I  PHE*     2.7    41.1    +      -       +      +
    254I  LEU*     4.3    17.0    -      -       +      -
    259I  ILE*     4.2    28.0    -      -       +      -
    262I  TRP*     5.4     2.7    -      -       +      -
    359I  LEU*     5.6     0.2    -      -       +      -
    360I  PHE*     1.3    82.7    -      -       -      +
    362I  VAL*     1.3    79.9    +      -       -      +
    363I  ARG*     4.5     7.0    -      -       +      +
    370I  VAL*     3.8    18.2    -      -       +      -
    372I  PHE      3.3     9.9    -      -       -      +
    373I  MET*     4.0    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 362 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171I  PHE*     3.8    30.3    -      -       +      -
    228I  TYR*     4.3     5.4    -      -       +      -
    233I  LEU*     4.3    13.5    -      -       +      -
    234I  SER      3.3    10.8    -      -       -      +
    235I  MET*     3.7    26.7    -      -       +      -
    326I  ILE*     5.2     0.2    -      -       +      -
    360I  PHE*     4.0     5.8    -      -       +      -
    361I  VAL*     1.3    86.2    -      -       -      +
    363I  ARG*     1.3    62.1    +      -       -      +
    370I  VAL*     3.8     1.2    -      -       -      -
    371I  LEU*     3.1    24.8    +      -       +      -
    372I  PHE*     3.0    40.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 363 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233I  LEU*     3.2    30.4    -      -       -      +
    234I  SER      2.9    12.1    +      -       -      +
    236I  PHE*     3.5    35.6    -      -       +      -
    259I  ILE*     3.7    18.4    -      -       +      +
    260I  SER*     3.9    21.5    +      -       -      +
    263I  LYS*     3.7    25.4    -      -       -      +
    361I  VAL*     4.6     5.2    -      -       +      -
    362I  VAL*     1.3    76.4    -      -       -      +
    364I  HIS*     1.3    64.9    +      -       -      +
    365I  ASN*     3.2    48.0    +      -       -      +
    368I  GLY*     4.0    18.2    -      -       -      +
    369I  THR      3.5    10.5    -      -       -      +
    370I  VAL*     5.4     1.6    -      -       +      -
    371I  LEU*     4.4     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 364 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78I  LEU*     4.4    11.5    -      -       +      +
     81I  GLU*     3.6    38.0    +      -       +      +
     82I  LEU*     5.5     6.3    -      -       +      -
     86I  TRP*     4.8     4.2    -      +       -      -
    232I  THR*     3.8     8.1    -      -       +      +
    233I  LEU*     3.8    19.5    -      -       +      -
    363I  ARG*     1.3    74.0    -      -       -      +
    365I  ASN*     1.3    51.4    +      -       -      +
    366I  PRO*     3.2    22.4    -      -       +      +
    367I  THR*     2.7    54.1    +      -       +      +
    368I  GLY      2.8    27.5    +      -       -      -
    369I  THR*     2.9    21.7    +      -       -      +
    371I  LEU*     4.3    10.8    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il